The number of people being referred to consultants with suspected cancer has fallen by about 50% during lockdown.
BBC Spotlight has obtained figures showing that during April and May there were 7,500 fewer "red flag" referrals than in the same months in 2019.
The number of hospital referrals by GPs for all conditions fell by 48,278.
Health Minister Robin Swann has acknowledged the damage done to normal services by the need to fight coronavirus.
On Tuesday morning, he is due to launch a blueprint for what he is describing as the rebuilding of the health service.
London-based cancer surgeon Luke Cascarini told Spotlight the problems being stored up for the NHS are concerning.
"Where are all the patients that we would have been treating if we hadn't been treating Covid?" he asked.
"I don't think there's any reason to think that the incidence of cancer has dropped over the last few months, so I think there's a big backlog.
"I think a lot of doctors are beginning to feel extremely proud of everything that's been done to cope with the crisis.
"I think we now need to deal with those undiagnosed or untreated cancers."
Spotlight will also reveal for the first time the parts of the scientific modelling on the pandemic which Robin Swann did not want shared with the public.
Spotlight is on BBC One Northern Ireland on Tuesday at 22:45 BST.